An intensive effort was directed toward examining the relationships between changes in viral burden, changes in viral genotype and phenotype, and changes in immunologic function in patients with human immunodeficiency virus (HIV) infection receiving a variety of anti- retroviral agents with different mechanisms of action alone or in combination. Isolates obtained from patients receiving zidovudine (ZDV) alone were found to develop ZDV resistance sooner than those from patients receiving ZDV in combination with interferon-alpha (IFN-alpha). In addition, the emergence of resistance was associated with a precipitous increase in the rate of CD4 decline. Neither ZDV nor IFN-` resistance were noted in patients receiving IFN-alpha alone. Studies of the nucleotide phosphonomethoxyethyl adenine (PMEA) and the immunotoxin CD4-Pseudomonas exotoxin (CD4-PE) were conducted for the first time in humans. Wild-type isolates were noted to have varying degrees of resistance to PMEA. PMEA resistance was mapped to amino acid 65 of the RT gene and found to confer cross-resistance to ddI. While active in vivo, PMEA therapy was associated with hepatic and genitourinary tract toxicities. In contrast, no activity was seen in the context of CD4-PE administration. A randomized, controlled trial of the non-nucleoside L697,661 demonstrated a dose-dependant development of resistance within 2 weeks of therapy that was determined to be due to a tyrosine to cysteine mutation at aa 181. New, RNA-based methods were evaluated for the monitoring of viral burden. An infectious clone of HIV underwent an 8-base pair insertion in the region of the LTR. This mutant virus was replication competent and served as an excellent internal control for the measurement of particle-associated RNA in plasma. The branched-DNA (bDNA) technique was found capable of quantitatively measuring changes in viral burden in large numbers of samples to a significantly greater degree than existing techniques. Changes in titers of plasma virus were found to fall within hours of initiation of anti-retroviral therapy and, utilizing a combination of PCR and bDNA, responses to combination anti- retroviral therapy with ddI, ZDV, and the non-nucleoside inhibitor U- 90,152S were clearly related to the pre-therapy presence of the 215 mutation of the RT gene.